#!/bin/bash

files='RGc19_S11 RGc18_S10 RGc16_S8 RGc20_S12 RGc14_S6 RGc15_S7 RGc17_S9'

for f in $files; do
    echo $f;
    # mkdir ../outputs/$f;
    salmon alevin -i ../ref_files/salmon_index -l ISR -1 ../data/raw/${f}_R1_001.fastq.gz -2 ../data/raw/${f}_R2_001.fastq.gz -p 8 -o ../outputs/salmon_alevin/${f}/ --chromiumV3 --sketch;
done
